Thanks a lot to take time to answer.
I kept equilibration because I just copy past the same file and change parameter and forgot to change the name at the beginning by "heating".
Actually my heating step doesn't work. It crashed at the beginning:
vlimit exceeded for step 0; vmax = 54.5176
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 35579 45871 45873
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
I had a look on my packmol input file and output file and I created a cubic box:
This is my input file:
tolerance 2.0
filetype pdb
output box_mix.pdb
structure WATER.pdb
number 2684
inside box 0. 0. 0. 90. 90. 90.
end structure
structure dmso.pdb
number 5560
inside box 0. 0. 0. 90. 90. 90.
end structure
And this is the input file from leap:
source leaprc.ff99SB
source leaprc.gaff
loadamberparams tripos1.frcmod
loadoff tripos1.lib
MOL = loadpdb box_mix.pdb
setbox MOL vdw
saveamberparm MOL mix.prmtop mix.inpcrd
savepdb MOL box_leap.pdb
quit
Am I wrong in the way to build my box?
Thanks you,
_______________________________________
De : Jason Swails [jason.swails.gmail.com]
Envoyé : lundi 24 février 2014 17:55
À : amber.ambermd.org
Objet : Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished
On Mon, 2014-02-24 at 17:22 +0000, Mele N. wrote:
> THe problem is I can' t see anything because I don' t get any output file. The mdcrd that I get at the end is empty.
> I can't pass any step during the heating.
I'm confused. You kept giving the 'equilibration' input file yet you
say the heating stage was the one having problems? If the heating stage
went fine, look at the output files from that step to see if anything
looks wrong (the "checkoverlaps" command in cpptraj can help when
looking for close contacts).
If the heating stage didn't work, look closely at the result from the
minimization step. I've also seen this type of error occur when the box
information is set incorrectly (e.g., did you build an octahedron box
with packmol but set your box to an orthorhombic shape in tleap? vice
versa?).
If the box information is wrong, then periodic images will most likely
overlap strongly and these errors are sure to occur.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 25 2014 - 02:30:03 PST
